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US: +1 908-268-9859
UK: +44 073-0653-7736

Summary

14 + years of research experience.
18 peer-reviewed publications to date.
35 bioinformatics tools developed.
12 + years of teaching/supervising experience.

Table of Contents

Education
Skills
Publications
Preprints
Acknowledgements
Reviewerships
Invited talks
Conference talks
Posters
Experience
Teaching
Software
Web apps
Websites
Grants
Awards
Affiliations
Extracurricular


CV source code

Updated Jan-31-2023

Main

Brian M. Schilder

Passionately pursuing multi-disciplinary research to improve human lives.

PhD Candidate

ScB, MPhil

Education

Imperial College London

PhD: Clinical Medical Research; Computational Neurogenomics

London, UK

2024

Thesis: Multi-omic medicine: dissecting the cell-type-specific molecular mechanisms underlying neurodegenerative disease genomics

The George Washington University

MPhil: Human Paleobiology; Evolutionary Neuroscience & Genomics

Washington, DC, USA

2017

Thesis: The evolution of the hippocampus and adult neurogenesis: Novel insights into the origins of human memory

Brown University

ScB: Cognitive Neuroscience; Neurological Diseases & Disorders

Providence, RI, USA

2011

Core Skills

Research

14+ years of highly multidisciplinary research experience. Creative and rapid hypothesis generation, project design, and problem solving.

N/A

  • Fields: Including but not limited to: Neuroscience, systems biology, bioinformatics, machine learning, multi-omics, biomedicine, cognition, statistics, computer science, phylogenetics, paleoanthropology biomechanics, primatology, histology/microscropy.
  • Publications: Strong writing skills as evidenced by 18 peer-reviewed scientific publications, 17 international conference posters and 10 sucessful grant applications.

N/A

Programming

Extensive experience in developing highly reproducible scripts and software packages to interrogate large and diverse data.

N/A

  • Bioinformatics: Including but not limited to: GWAS, QTL, bulk/scRNA-seq & epigenomics, machine learning, high-performance computing, GitHub, GitHub Actions, Docker/Singularity containers, DockerHub, conda, Nextflow, reproducibility.
  • R: Created 26 R packages to date, including on Bioconductor and CRAN. Experienced in created Shiny Apps and Rmarkdown reports.
  • Python: Regularly uses ML packages (e.g. sklearn, tensorflow, Keras). Developed and own IP for PubReporter, a software for extracting and conducting topic modelling/NLP on relevant scientific literature at scale.
  • Javascript/HTML/CSS: Created 10+ websites, web apps, and interactive reports. Developed templates to automatically render websites on-the-fly from CSVs using Javascript.

N/A

Communication

Effective and engaging scientific presentations to a variety of audiences.

N/A

  • Peers: Extensive experience presenting research proposals/findings to both internal and external labs/conferences. Invited speaker at leading research institutions. Diverse, multi-disciplinary and global collaborative network.
  • Students: Teaching assistant and/or guest lecturer for courses in diverse fields (biological anthropology, neuroscience, computational biology).
  • Public: Developed and delivered numerous community engagement programs for a wide variety of stakeholders, including students (preschool through postgraduate), community members, and patients (e.g. Children’s National Hospital, Parkinson’s UK).

N/A

Project Management

Coordinates multiple independent projects at once with researchers of varying degrees of education and research experience. Effective handling of many projects at once.

N/A

  • Documentation: Detailed and understandable in-code documentation is second-nature.
  • Version control: Extensive and daily use of git, GitHub Issues, GitHub Projects.
  • Supervision: Supervises numerous student research projects.

N/A

Publications

Dissecting the Shared Genetic Architecture of Suicide Attempt, Psychiatric Disorders, and Known Risk Factors

Biological Psychiatry (2022) 91(3):313-327; https://doi.org/10.1016/j.biopsych.2021.05.029

N/A

2022

N Mullins, J Kang, AI Campos,…BM Schilder, et al. 

Multi-omic insights into Parkinson’s Disease: From genetic associations to functional mechanisms

Neurobiology of Disease (2021) 105580; https://doi.org/10.1016/j.nbd.2021.105580

N/A

2021

BM Schilder, E Navarro, T Raj

Fine-Mapping of Parkinson’s Disease Susceptibility Loci Identifies Putative Causal Variants

Human Molecular Genetics (2021) ddab294; https://doi.org/10.1093/hmg/ddab294

N/A

2021

BM Schilder, T Raj

echolocatoR: An Automated End-to-End Statistical and Functional Genomic Fine-Mapping Pipeline

Bioinformatics (2021) btab658; https://doi.org/10.1093/bioinformatics/btab658

N/A

2021

BM Schilder, J Humphrey, T Raj

MungeSumstats: A Bioconductor Package for the Standardisation and Quality Control of Many GWAS Summary Statistics

Bioinformatics (2021) 37(23):4593-4596; https://doi.org/10.1093/bioinformatics/btab665

N/A

2021

A Murphy, BM Schilder, NG Skene

Dysregulation of mitochondrial and proteo-lysosomal genes in Parkinson’s disease myeloid cells

Nature Genetics (2021) https://doi.org/10.1101/2020.07.20.212407

N/A

2021

E Navarro, E Udine, K de Paiva Lopes, M Parks, G Riboldi, BM Schilder…T Raj
News
- Mount Sinai: Fighting Neurodegenerative Disorders (Mount Sinai Health System, 2019)

Phenome-wide and eQTL Associations of COVID-19 Genetic Risk Loci

iScience (2021) https://doi.org/10.1016/j.isci.2021.102550

N/A

2021

C Moon, BM Schilder, T Raj, K-l Huang

Genome-Wide Association Study of over 40,000 Bipolar Disorder Cases Provides Novel Biological Insights

Nature Genetics (2020) 53:817-829; https://doi.org/10.1038/s41588-021-00857-4

N/A

2020

N Mullins, AJ Forstner, KS O’Connell, B Coombes, JRI Coleman…BM Schilder… et al.

Tensor decomposition of stimulated monocyte and macrophage gene expression profiles identifies neurodegenerative disease-specific trans-eQTLs

PLOS Genetics (2020) 16(9):e1008549; https://doi.org/10.1101/499509

N/A

2020

S Ramdhani, E Navarro, E Udine, AG Efthymiou, BM Schilder, M Parks, A Goate, T Raj
News
- Researchers identify 64 regions of the genome that increase risk for bipolar disorder (EurekAlert, 2021)
- Largest Bipolar Disorder Genetics Study Doubles Genetic Risk Factors (Nordic Society of Human Genetics and Precision Medicine, 2021)

Evolutionary shifts dramatically reorganized the human hippocampal complex

Journal of Comparative Neurology (2019) 528(17):3143-3170; https://doi.org/10.1002/cne.24822

N/A

2019

BM Schilder, HM Petry, PR Hof

FAIRshake: Toolkit to Evaluate the Findability, Accessibility, Interoperability, and Reusability of Research Digital Resources

Cell Systems (2019) 9; https://doi.org/10.1016/j.cels.2019.09.011

N/A

2019

D Clarke, L Wang, A Jones, M Wojciechowicz, D Torre, K Jagodnik, S Jenkins, P McQuilton, Z Flamholz, M Silverstein, BM Schilder…A Ma’ayan
News
- Chosen as ‘Featured Frontmatter’ article in Cell Systems

Geneshot: search engine for ranking genes from arbitrary text queries

Nucleic Acids Research (2019) 47(W1):W571-W577; https://doi.org/10.1093/nar/gkz393

N/A

2019

A Lachmann, BM Schilder, ML Wojciechowicz, D Torre, MV Kuleshov, AB Keenan, A Ma’ayan
News
- Geneshot: Piercing the Literature to Identify and Predict Relevant Genes (University of Pittsburgh Health Sciences Library System Update, 2019)
- The Future of AI at the Hasso Plattner Institute for Digital Health at Mount Sinai (Mount Sinai Health System, 2020)

eXpression2Kinases (X2K) Web: linking expression signatures to upstream cell signaling networks

Nucleic Acids Research (2018) 46(W1):W171-W179; https://doi.org/10.1093/nar/gky458

N/A

2018

DJB Clarke, MV Kuleshov, BM Schilder, D Torre, ME Duffy, AB Keenan, A Lachmann, AS Feldmann, GW Gundersen, MC Silverstein, Z Wang
News
- Mount Sinai Faculty Spotlight: Ma’ayan Lab (Mount Sinai Health System, 2018)

Defining elemental imitation mechanisms: A comparison of cognitive and motor-spatial imitation learning across object- and computer-based tasks

Journal of Cognition and Development (2015) 17(2):221-243; https://doi.org/10.1080/15248372.2015.1053483

N/A

2015

F Subiaul, L Zimmerman, E Renner, BM Schilder, R Barr

Take the monkey and run

Journal of Neuroscience Methods (2015) 248:28-31; http://doi.org/10.1016/j.jneumeth.2015.03.023

N/A

2015

KA Phillips, MK Hambright, K Hewes, BM Schilder, CN Ross, SD Tardif

Becoming a high-fidelity - super - imitator: what are the contributions of social and individual learning?

Developmental Science (2014) 18(6):1025-1035; http://doi.org/10.1111/desc.12276

N/A

2014

F Subiaul, EM Patterson, BM Schilder, E Renner, R Barr

Working memory constraints on imitation and emulation

Journal of Experimental Child Psychology (2014) 128:190-200; http://doi.org/10.1016/j.jecp.2014.07.005

N/A

2014

F Subiaul, BM Schilder

Preprints

The rworkflows suite: automated continuous integration for quality checking, documentation website creation, and containerised deployment of R packages

Research Square (2023) https://doi.org/10.21203/rs.3.rs-2399015/v1

N/A

2023

BM Schilder, AE Murphy, NG Skene

CUT&Tag recovers up to half of ENCODE ChIP-seq peaks

bioRxiv (2022) https://doi.org/10.1101/2022.03.30.486382

N/A

2022

D Hu, L Abbasova, BM Schilder, A Nott, NG Skene, SJ Marzi

EpiCompare: R package for the comparison and quality control of epigenomic peak files

bioRxiv (2022) https://doi.org/10.1101/2022.07.22.501149

N/A

2022

S Choi, BM Schilder, L Abbasova, AE Murphy, NG Skene

Acknowledgements

eQTL Catalogue: a compendium of uniformly processed human gene expression and splicing QTLs.

Nature Genetics (2021) 53:1290-1299; https://doi.org/10.1038/s41588-021-00924-w

N/A

2021

N Kerimov, JD Hayhurst, K Peikova et al.

Functionally-informed fine-mapping and polygenic localization of complex trait heritability

Nature Genetics (2020) https://doi.org/10.1038/s41588-020-00735-5

N/A

2020

O Weissbrod…AL Price

Wayfinding: The science and mystery of how humans navigate the world.

St. Martin’s Press (2019) ISBN-13: 978-1250096968; https://www.amazon.co.uk/Wayfinding-Science-Mystery-Humans-Navigate/dp/1250096960

N/A

2019

MR O’Connor

EEG oscillations reveal neural correlates of evidence accumulation

Frontiers in Decision Neuroscience (2012) 6(106):Jan-13; https://doi.org/10.3389/fnins.2012.00106

N/A

2012

M van Vugt, P Simen, L Nystrom, P Holmes, J Cohen

Trial-by-trial adaptation of decision making performance: a model-based EEG analysis

Interdisciplinary Perspectives on Cognition, Education, and the Brain (2011) 7; https://www.semanticscholar.org/paper/Trial-by-trial-adaptation-of-decision-making-a-EEG-Vugt-Simen/330371d08842ecd1bda332dd22351a7135b5cb1f

N/A

2011

M van Vugt, P Simen, J Cohen

Reviewerships

PLOS Genetics

1 article

N/A

N/A

.

Alzheimer’s Research & Therapy

1 article

N/A

N/A

.

Bioinformatics

2 articles

N/A

N/A

.

Invited Talks

Decomposing the phenome: learning the latent genomic structure underlying thousands of diseases and traits

Neuroepidemiology of Aging Webinar
RUSH Alzheimer’s Disease Center (RADC)
RUSH University

N/A

2022

Drug (re)discovery in the age of genomics: multi-omic strategies for identifying disease treatments

Department Seminar
3D (Drug, Disease, Delivery) Center / Department of Pharmaceutical Sciences
University of South Dakota

N/A

2022

Statistical and functional genetic fine-mapping across multiple disease

Seminar
Alzheimer’s Disease Sequencing Project
Columbia University / Icahn School of Medicine at Mount Sinai

N/A

2020

Statistical and functional genetic fine-mapping across multiple disease

Laboratory of Neurogenetics Friday Workshop
National Institute on Aging
National Institutes of Health

N/A

2020

Conference Talks

Systematic quantification of animal model viability across human diseases

Informatics-Synapse Joint Early Career Researcher Meeting

UK Dementia Research Institute (UK DRI)

N/A

2022

Automated genetic fine-mapping of neurological disorders

London Genetics Network

N/A

2020

Parkinson’s disease derived monocytes show alteration in the phago-lysosomal pathway

American Society of Human Genetics

N/A

2019

Co-contributor

Marmoset Social

Society for Neuroscience

N/A

2016

JB Johnston Club for Evolutionary Neuroscience

Society for Neuroscience

N/A

2016

JB Johnston Club for Evolutionary Neuroscience

Society for Neuroscience

N/A

2014

Conference Posters

Systematic quantification of animal model viability across human disease

Rising Scientist Day at Imperial College London (2022)

N/A

2022

BM Schilder, NG Skene

Cell-type-specific reconstruction of primate evolution from genomic positive selection

Rising Scientist Day at Imperial College London (2020)

N/A

2020

K Murphy, BM Schilder, NG Skene

Automated genetic and functional fine-mapping of Parkinson’s Disease Loci.

American Society of Human Genetics (2019)

N/A

2019

BM Schilder, T Raj

Parkinson’s disease derived monocytes show alteration in the phago-lysosomal pathway

American Society of Human Genetics (2019)

N/A

2019

E Udine, E Navarro, …BM Schilder, …T Raj

Learning X2K: Parameter Optimization via Genetic Algorithms to Calibrate the Expression2Kinases Pipeline

Illuminating the Druggable Genome (2018)

N/A

2018

BM Schilder, A Lachmann, M Kuleshov, A Ma’ayan

Learning X2K: Parameter Optimization via Genetic Algorithms to Calibrate the Expression2Kinases Pipeline

Big Data 2 Knowledge - Library of Integrated Network-Based Cellular Signatures (LINCS) (2018)

N/A

2018

BM Schilder, A Lachmann, M Kuleshov, A Ma’ayan

The evolution of the human hippocampus and neuroplasticity

Association for American Physical Anthropologists (2017)

N/A

2017

BM Schilder, BJ Bradley, CC Sherwood

The molecular evolution of the primate hippocampus

Society for Neuroscience (2016)

N/A

2016

BM Schilder, BJ Bradley, CC Sherwood

Effects of exercise on disease progression and cognition in the marmoset EAE model

JB Johnston Club for Evolutionary Neuroscience (2015)

N/A

2015

KA Phillips, MK Hambright, K Hewes, BM Schilder, B Jagessar, B t’Hart, SD Tardif

Individual, Observational, and Imitation Learning in Orangutans and Children

Association for American Physical Anthropologists (2015)

N/A

2015

E Renner, BM Schilder, F Subiaul

The helper hinderer task revisited: an infant eye tracking study

The George Washington University Research Day (2014)

N/A

2014

A Gokhale, BM Schilder, F Subiaul

Dendritic morphology of pyramidal neurons across the visual stream: A direct comparison of chimpanzees and humans

Society for Neuroscience (2013)

N/A

2013

BM Schilder, O Adeyo

The striatum in the evolution of learned vocalizations: Understanding the neurobiological precursors to human speech using a chimpanzee model

Society for Neuroscience (2013)

N/A

2013

S Bianchi, T Duka, G Muntane, BM Schilder, CD Stimpson, WD Hopkins

Imitation & emulation in a novel box task

Association for Psychological Science (2013)

N/A

2013

L Zimmerman, N Brito, C Mendelson, R Barr, E Renner, BM Schilder, F Subiaul

A study of imitation and working memory in 2- to 4- year-olds

Association for Psychological Science (2013)

N/A

2013

R Barr, F Subiaul, L Zimmerman, L Renner, BM Schilder, C Mendelson, L Golojuch

The impact of wealth on sharing preferences in children

Child Development Society (2013)

N/A

2013

J Miller, BM Schilder, L Peizer, F Subiaul

Research Experience

PhD Candidate

Imperial College London (UK Dementia Research Institute, Department of Brain Sciences)

London, UK

2024 - 2020

  • Thesis: Multi-omic medicine: dissecting the cell-type-specific molecular mechanisms underlying neurodegenerative disease genomics.
  • Objective: Computationally dissect the subtraits, cell-types underlying the genomic signatures of Alzheimer’s Disease and Parkinson’s Disease.

Consultant

120/80 MKTG

New York, NY, USA

- - 2019

  • Offers consultation services to a wide portfolio of high-profile digital healthcare companies, with a focus on data analytics, research publication, and strategic transparency.
  • Provides data-driven business intelligence reports using proprietary software scientific literature mining software that I have created.
  • Professional company web design.

Bioinformatician II

Icahn School of Medicine at Mount Sinai (Department of Neuroscience / Department of Neurology / Department of Genetics & Genomics / Ronald M. Loeb Center for Alzheimer’s Disease)

New York, NY, USA

2020 - 2018

  • Developed machine learning systems to integrate large-scale multi-omics datasets (e.g. whole-genome sequencing, bulk and single-cell RNA-seq, epigenomics, clinical data) to uncover the molecular mechanisms underlying neurodegenerative diseases (e.g. Alzheimer’s, Parkinson’s, ALS).
  • Computationally identified specific disease-causal variants, pathways and cell-types for subsequent functional wet lab validation (e.g. CRISPR-cas9 editing in patient-derived cell cultures, iPSCs and cerebral organoids).

Bioinformatician II

Icahn School of Medicine at Mount Sinai (Department of Pharmacological Sciences)

New York, NY, USA

2018 - 2017

  • Conducted computational systems biology research. Integrated and analyzed large-scale genomic and biomedical data (e.g. Python, R, JavaScript).
  • Developed evolutionary algorithm to optimize gene network kinase regulator prediction (eXpression2Kinases).
  • Developed and deployed computational tools, software, databases and web applications for basic and clinical research, resulting in 3 peer-reviewed publications.

Participant

Technische Universität Dresden / eMed (Summer School in Systems Medicine)

Frauenchiemsee, Germany

2017

  • Attended lectures and extended skills in extraction and analysis of big data from biomedical and neurogenomic resources.
  • Developed, performed and wrote manuscript for collaborative bioinformatics research project in less than one week.

Participant

Icahn School of Medicine at Mount Sinai (Scientific Computing & Data Science)

New York, NY, USA

2016

  • Intensive summer school in high-performance computing, coding, genome database utilization and bioinformatics methods including transcriptomics and genetic association testing.

Graduate Student

The George Washington University (Department of Anthropology)

Washington, DC, USA

2017 - 2013

  • Thesis: Evolution of the Hippocampus and Adult Neurogenesis Research
  • Investigated the evolution of human-specific cognitive abilities and neurological disease susceptibilities (e.g. Alzheimer’s Disease).
  • Focused on neuroanatomical, transcriptomic and genomic evolution of the human hippocampus and memory.

Collaborator

Trinity University / Southwestern National Primate Research Center (Department of Neuroscience)

San Antonio, TX, USA

2017 - 2014

  • Investigated the neurobiological mechanisms underlying the ameliorating effects of exercise on relapse-remitting Multiple Sclerosis.

Teaching Assistant / Project Leader

The George Washington University / Rutgers University (Department of Anthropology)

Ileret, Kenya

2014

  • Served as Teaching Assistant while excavating Lower Paleolithic hominin sites (Homo, Paranthropus).
  • As Project Leader, investigated the running biomechanics of local Daasanach tribespeople while mentoring undergraduate students.

Research Assistant

The George Washington University (Department of Anthropology)

Washington, DC, USA

2013 - 2011

  • Performed dissection, histology, microscopy and quantitative stereology in post-mortem primate brain tissues.
  • Trained junior and senior personnel on lab protocols.

Senior Lab Manager

The George Washington University (Department of Speech, Language & Hearing Sciences)

Washington, DC, USA

2013 - 2011

  • Organized and trained dozens of undergraduates to conduct weekly cognitive development research; designed and/or directly contributed to over 15 research projects in two years.

Volunteer Researcher

University of Winnipeg / University of Belgrade (Department of Anthropology / Department of Archaeology)

Sićevo, Serbia

2012

  • Excavated Paleolithic fossils and tools (H. heidelbergensis, H. neanderthalensis) at Mala Balanica, Velika Balanica, and Pešturina sites.

Volunteer Researcher

Universidad de Murcia (Department of Zoology & Physical Anthropology)

Murcia, Spain

2011

  • Excavated Paleolithic fossils and tools from Cueva Negra (H. heidelbergensis) and Sima de las Palomas (H. neanderthalensis) with an international research team.

Volunteer Research Intern

American Museum of Natural History (Division of Anthropology)

New York, NY, USA

2011

  • Contributed to paleoanthropological research on primate fossils using 3D morphometry imaging equipment including Minolta, Microscribe and CT.

Student Researcher

Brown University (Department of Cognitive, Linguistic & Psychological Sciences)

Providence, RI, USA

2010 - 2009

  • Experimental Analysis of Animal Behavior & Cognition: Conducted various operant conditioning experiments on rats. Gained experience in animal behavioral training, data collection, and data analysis in MATLAB.
  • Laboratory in Genes and Behavior: Tested transgenic mice with modified N-type voltage-gated calcium channel subunits in a battery of cognitive and sensorimotor tasks. Results were published.

Teaching / Mentoring Experience

Research Mentor

Imperial College London (Department of Brain Sciences / Department of Life Sciences)

London, UK

- - 2020

  • Mentored students and affiliated projects:
  • Kitty Murphy (PhD): ‘Evolutionary pressures on cell types: leveraging species differences to gain insight into neurodegenerative disease risk’
  • Sheen Lei (BSc): ‘Benchmarking cell-type-specific enrichment of genome-wide disease signatures’
  • Ted Reese (MSc): ‘Computational cell-type annotation of single-cell epigenomics data’
  • Xindong Sun (MSc): ‘Benchmark of Targeted insertion of promoters sequencing (TIP-seq) on histone modification H3K27ac and H3K27me3 in K562 cell line’
  • Shuhan Shen (MSc): ‘Evaluation and optimisation of methods for identifying the cell types underlying genetic disease signatures’
  • Lusheng Li (MSc): ‘Genetic identification of cell types underlying mammalian phenotypes’
  • Sera Choi (BSc): ‘EpiCompare: R package for QC and benchmarking epigenetic datasets’
  • Emilie Cottard (MSc) & Will Lunt (BSc): ‘A meta-analysis of selective cell-type vulnerability in Parkinson’s Disease neuropathology’
  • Jai Chapman (BSc): ‘Expression Weighted Cell Type Enrichment as a Tool for Identifying Cell Types Underlying Rare Disease Phenotypes’
  • Bobby Gordon-Smith (MSc): ‘Identification of cell types involved in rare disease-associated human phenotypes’
  • Leyla Abbasova (MSc): ‘Analysis and optimisation of CUT&Tag for epigenomic profiling of the brain’
  • Barney Hill (BSc): ‘Identification of cell-types associated with latent factors inferred from phenome-wide GWAS summary statistics’

Research Mentor

Icahn School of Medicine at Mount Sinai (Department of Neuroscience / Department of Neurology / Department of Genetics & Genomics / Ronald M. Loeb Center for Alzheimer’s Disease)

New York, NY, USA

2020 - 2019

  • Mentored MS, MD, and PhD students in projects focused on computational exploration of phenotype clustering and genomic regulation of neurodegenerative diseases.

Research Co-mentor

Icahn School of Medicine at Mount Sinai (Department of Pharmacological Sciences)

New York, NY, USA

2018

  • Mentored students and affiliated projects:
  • Vivian Utti (BSc): ‘ChEA3: Transcription Factor Enrichment Analysis’ as part of the Summer Research Training Program in Biomedical Big Data Science.
  • Mary Duffy (PhD): ‘Predicting upstream kinase regulators from interaction network databases’
  • Zach Flamholz (BSc): ‘modEnrichr: a suite of gene set enrichment analysis tools for model organisms’

Guest Lecturer

Icahn School of Medicine at Mount Sinai (Department of Pharmacological Sciences)

New York, NY, USA

2018

  • Lectured on data visualization in Python and Jupyter notebooks in the PhD/MD course ‘Programming for Big Data Biomedicine’.

Research Mentor

The George Washington University (Department of Anthropology)

Washington, DC, USA

2017 - 2016

  • Mentored students and affiliated projects:
  • Jamie Kleiner (BSc): ‘Animal model simulating MS and exercise’s impact on adult hippocampal neurogenesis’

Teaching Assistant

The George Washington University (Department of Anthropology)

Washington, DC, USA

2015

  • Course: ‘Human Brain Evolution’
  • Guest lectured, graded all assignments and exams, and provided additional educational support during office hours.

Teaching Assistant

The George Washington University (Department of Psychology)

Washington, DC, USA

2014

  • Course: ‘Biological Psychology’
  • Led undergraduates in article discussions, graded all assignments and exams, and provided additional educational support during office hours.

Teaching Assistant

The George Washington University (Department of Anthropology)

Washington, DC, USA

2014 - 2013

  • Course: ‘Biological Anthropology’
  • Led undergraduate students in two, 2-hour lab sessions per week, graded lab assignments and exams, and provided additional educational support during office hours.

Research Mentor

The George Washington University (Department of Psychology)

Washington, DC, USA

2013 - 2012

  • Mentored students and affiliated projects:
  • Anushka Gokhale (BSc): ‘Infants’ Social Assessment of Characters Through Eye Gaze’

Lab Protocol Trainer

The George Washington University (Department of Anthropology)

Washington, DC, USA

2013 - 2011

  • Trained undergraduate, graduate, and post-doctoral researchers in Social Cognition Lab and Lab for Evolutionary Neuroscience in a variety of methodological research protocols.

Software Packages

rworkflows

Continuous integration for R packages. Automates testing, documentation website building, and containerised deployment
https://github.com/neurogenomics/rworkflows
https://doi.org/10.21203/rs.3.rs-2399015/v1

N/A

1.

TIPseeker

R package for post-processing [single-cell] TIP-seq data
https://github.com/neurogenomics/TIPseeker

N/A

2.

PeakyFinders

R package for mining, calling, and importing epigenomic peaks
https://github.com/neurogenomics/PeakyFinders

N/A

3.

SkillNet

Creates user-specific contribution networks from GitHub Organization repositories
https://github.com/neurogenomics/SkillNet

N/A

4.

phenomix

R package for the exploration and analysis of many genotype-phenotype datasets at once
https://github.com/neurogenomics/phenomix

N/A

5.

MAGMA_Celltyping

Identify cell types underlying the associations found in GWAS summary statistics
https://github.com/neurogenomics/MAGMA_Celltyping

N/A

6.

EWCE

Expression Weighted Celltype Enrichment
https://github.com/NathanSkene/EWCE

N/A

7.

EpiCompare

R package for QC and benchmarking epigenetic datasets
https://github.com/neurogenomics/EpiCompare

N/A

8.

MultiEWCE

R package for analysing multiple gene lists using EWCE
https://github.com/neurogenomics/MultiEWCE

N/A

9.

HPOExplorer

Functions for working with the Human Phenotype Ontology data
https://github.com/neurogenomics/HPOExplorer

N/A

10.

orthogene

Interspecies gene mapping
https://github.com/neurogenomics/orthogene

N/A

11.

MungeSumstats

Standardise the format of summary statistics from GWAS
https://github.com/neurogenomics/MungeSumstats
https://doi.org/10.1093/bioinformatics/btab665

N/A

12.

scNLP

Tools for applying natural language processing (NLP) techniques to single-cell (sc) omics data
https://github.com/neurogenomics/scNLP

N/A

13.

scKirby

Automated ingestion and conversion of various single-cell data formats
https://github.com/neurogenomics/scKirby

N/A

14.

echolocatoR

R package for end-to-end statistical and functional fine-mapping with extensive dataset access
https://github.com/RajLabMSSM/echolocatoR
https://doi.org/10.1093/bioinformatics/btab658

N/A

16.

echodata

Examples of fine-mapped GWAS summary statistics, data formatting functions, and API access to the echolocatoR Fine-mapping Portal
https://github.com/RajLabMSSM/echodata

N/A

17.

echoannot

Functions for annotating genomic data with annotations and epigenomic data
https://github.com/RajLabMSSM/echoannot

N/A

18.

echoplot

R package for LocusZoom-inspired GWAS/QTL visualization, with API access to LD panels
https://github.com/RajLabMSSM/echoplot

N/A

19.

echoconda

Various utility functions to find, build, and use conda environments from within R
https://github.com/RajLabMSSM/echoconda

N/A

20.

echotabix

Tabix indexing and querying
https://github.com/RajLabMSSM/echotabix

N/A

21.

echoLD

LD downloading and processing.
https://github.com/RajLabMSSM/echoLD

N/A

22.

echodeps

Creates interactive dependency networks for R packages.
https://github.com/RajLabMSSM/echodeps

N/A

23.

echogithub

Access and process metadata from GitHub
https://github.com/RajLabMSSM/echogithub

N/A

24.

downloadR

Single- and multi-threaded downloading functions
https://github.com/RajLabMSSM/downloadR

N/A

25.

catalogueR

R package for rapid API-access and colocalization of summary statistics from eQTL Catalogue
https://github.com/RajLabMSSM/catalogueR

N/A

26.

PubReporter

Proprietary Python package for extracting relevant scientific literature and citations, performing topic modelling, and generating interactive business intelligence reports.

N/A

27.

Web Apps

Geneshot

Flexible tool to identify genes associated with any biomedical term and to predict novel target genes
http://amp.pharm.mssm.edu/geneshot
https://doi.org/10.1093/nar/gkz393

N/A

1.

X2K

eXpression 2 Kinases (X2K) Web: Automated computational pipeline to infer kinase regulators from weighted or unweighted gene lists
http://amp.pharm.mssm.edu/X2K
https://doi.org/10.1093/nar/gky458

N/A

2.

Rare Disease Celltyping Apps

Web portal connecting to multiple R Shiny apps to explore, visualize, and download cell type-specific enrichment results and systematically prioritised gene targets for over 6,000 rare disease phenotypes.
https://github.com/neurogenomics/rare_disease_celltyping_apps

N/A

3.

Parkinson’s Disease Omics Review

Data and code associated with the Parkinson’s Disease review paper by Schilder, Navarro & Raj (Neurobiology of Disease, 2021)
https://github.com/RajLabMSSM/PD_omics_review
https://rajlabmssm.github.io/PD_omics_review/
https://doi.org/10.1016/j.nbd.2021.105580

N/A

4.

Selective Vulnerability Meta-analysis

Selective Vulnerability Meta-analysis: Shiny app dedicated to the exploration and dissemination of meta-analysed cell counts manually curated and harmonised from the Parkinson’s Disease literature
https://github.com/neurogenomics/SelectiveVulnerabilityMetaAnalysis

N/A

5.

echolocatoR Fine-mapping Portal

Access to interactive plots and fine-mapping results across many GWAS/QTL datasets using echolocatoR
https://github.com/RajLabMSSM/Fine_Mapping_Shiny
https://rajlab.shinyapps.io/Fine_Mapping_Shiny
https://doi.org/10.1093/bioinformatics/btab658

N/A

6.

Tensor Decomposition Shiny App

Interactive application to explore and download all results and plots from Ramdhani et al. (PLOS Genetics, 2020)
https://github.com/RajLabMSSM/Tensor_myeloid
https://rajlab.shinyapps.io/Tensor_myeloid
https://doi.org/10.1101/499509

N/A

7.

Hippocampal Evolution

Interactive code, results and visualization for the manuscript “Evolutionary selective pressures dramatically expanded and reorganized the human hippocampal complex”
https://github.com/bschilder/Hippo_Eco
https://bschilder.github.io/Hippo_Eco/HPsubfield_eco
https://doi.org/10.1002/cne.24822

N/A

8.

Websites

Grants

Total (all grants): $2,949,052
Total (as primary applicant): $310,562

N/A

N/A


N/A

Imperial UK Research Institute Impact Acceleration Account,
Imperial College London

Project: ‘Creating commercial kit solutions for single cell epigenetic profiling of histone marks and transcription factors’

N/A

2023

  • Role: Co-applicant
  • PI: NG Skene
  • Amount: £80,000

Turing Community Award,
Alan Turing Institute

Project: ‘Multi-omic medicine: dissecting the cell-type-specific molecular mechanisms underlying neurodegenerative disease genomics’

N/A

2024 - 2022

  • Role: Primary applicant
  • PI: BM Schilder
  • Amount: £3,000

National Institutes of Health

Project: ‘Statistical and functional fine-mapping of bipolar disorder genetic risk loci’

N/A

2022

  • Role: Co-applicant
  • PI: N Mullins

Collaborative Single Cell and Spatial Transcriptomics Studies Award Programme,
UK Dementia Research Institute

Project: ‘Amplifying genome coverage of single cell epigenetic profiling of the human brain’

N/A

2021

  • Role: Co-applicant
  • PI: D Hu, NG Skene
  • Amount: £12,790

National Institutes of Health

Project: “Cognitive Systems Analysis of Alzheimer’s Disease Genetic and Phenotypic Data”

N/A

2020

  • Role: Co-applicant
  • PI: T Raj, D Knowles
  • Amount: $2,523,431

UK Dementia Research Institute

Project: ‘UK DRI at Imperial Distinguished Studentship’

N/A

2024 - 2020

  • Role: Primary applicant
  • PI: BM Schilder
  • Amount: £217,000

The Michael J. Fox Foundation

Project: “The Role of Peripheral Myeloid Cells in Parkinson’s Disease”

N/A

2019 - 2017

  • Role: Fundee
  • PI: T Raj

The Michael J. Fox Foundation

Project: ‘Functional Fine-Mapping of LRRK2 Locus’

N/A

2020 - 2017

  • Role: Fundee
  • PI: T Raj

National Science Foundation

Project: ‘The evolution of the hippocampus and adult neurogenesis: novel insights into the origins of human memory’

N/A

2017

  • Role: Primary applicant
  • PI: BM Schilder
  • Amount: $31 543

Wenner-Gren

Project: ‘The evolution of the hippocampus and adult neurogenesis: insights into the origins of human memory’

N/A

2017

  • Role: Primary applicant
  • PI: BM Schilder
  • Amount: $19,512

Leakey Foundation

Project: ‘The evolution of the hippocampus and adult neurogenesis: Novel insights into the origins of human memory’

N/A

2016

  • Role: Primary applicant
  • PI: BM Schilder
  • Amount: $15,000

COSMOS Club

Project: ‘The evolution of adult neurogenesis across primates’

N/A

2016

  • Role: Primary applicant
  • PI: BM Schilder
  • Amount: $3,250

Awards

Prize for Computational Reproducibility in Dementia Research,
UK Dementia Research Institute

Project: ‘MungeSumstats: A Bioconductor package for the standardisation and quality control of many GWAS summary statistics’

N/A

2022

Award for Outstanding Contribution,
NEUROHACK, Deep Dementia Phenotyping Network (DEMON)

Project: ‘Predicting ALS drug targets using integrative multi-modal deep learning’

N/A

2022

News
- Individually awarded for outstanding contributions during the NEUROHACK 2022, a competitive 4-day hackathon to apply AI in finding ALS therapeutic solutions.

Prize for Computational Reproducibility in Dementia Research,
UK Dementia Research Institute

Project: ‘echolocatoR: an automated end-to-end statistical and functional genomic fine-mapping pipeline’

N/A

2021

Centre Photography Competition,
UK Dementia Research Institute

Project: ‘Wildfire Circle, Golden Brain, Wildfire, Geneshot, Geology of Biology, Neon Brain’

N/A

2021

Art of the Brain,
Friedman Brain Institute, Icahn School of Medicine

Project: ‘Wildfire’

N/A

2019

News
- Awarded 2nd place and Featured on the cover of Biological Psychiatry: Volume 87, Issue 12 (2020). Exhibited and auctioned at the Grady Alexis Gallery (New York City), where all proceeds were voluntarily donated to the Diversity in Neuroscience Initiative.

Affiliations

Imperial College London

  • Department of Brain Sciences
  • Faculty of Medicine

N/A

UK Dementia Research Institute (UK DRI)

  • Synapse Working Group
  • Informatics Working Group

N/A

Deep Dementia Phenotyping Network (DEMON)

  • Genetics & Omics Working Group
  • Experimental Models Working Group
  • Drug Discovery & Trials Optimisation Working Group

N/A

Psychiatric Genomics Consortium (PGC)

  • Bipolar Disorder Working Group

N/A

Bioconductor Developers Community

  • Bioconductor Cloud Methods Working Group
  • Active developer

N/A

Extracurricular Experience

Competitive Running Career

Earth

.

- - 2003

Music Production

  • Writes, records, produces and performs original music.
  • Instruments: keys, percussion, vocals, etc.
  • Proficient in Logic Pro X Digital Audio Workstation (DAW).
  • Experiments with generative AI.

Earth

.

- - 1995

Visual Art

Earth

.

- - 2015